MultiFile Add-on with single python file
Please see the included add-ons that come with Blender as examples. If you are on Windows, that will most likely be C:\Program Files\Blender Foundation\Blender [version number]\[version number]\scripts\addons\
If you go to any of the folders there, you will see what would be in the zip file if it was a zipped addon:

The main addon file is __init__.py, you have to have one like that.